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Virology Computing

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Problems

Computing 1: Intro to Virology & Models

Keeping a log

Computing 2: Bioinformatics Searching

Focus of exercises

Computing 3: Bioinformatics Project

Using WebCT

The Great Paper Chase

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Introduction

To those of you who have already embraced the Information Age: You should find that the web-based instructional support and learning activities will be a fun enrichment to the course.

To those of you who have not yet driven the Information Superhighway, or only tried it a few times: You may find some of this intimidating at first. However, after exploring these pages and working through the exercises, your comfort level will increase. The secondary gain will be that as you gain expertise in virology, your computing skills will increase as well.

To all: Problems will occur. Links to specified sites may change. A page on this site may not load properly. Unique problems may surface associated with specific server access. An analysis application may crash or give consistent error messages. Whatever it is, please communicate- both with me and with your fellow classmates. The first forum topic I have posted [click on "Interactive", go to "Discussion Fora"] is titled "Computer problems". If you have a problem, make a posting. Check the forum frequently. If you see where you can contribute a solution, please do. You may find an answer to your problem in someone else's posting. If the problem is associated with a campus computer, or if you think it may be due to the SSU server, or even if you are not sure, try the help line: 664-HELP.

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Keeping a log: It is easy to get caught up in surfing the web, but how do you keep track of all the places you'd like to come back to? How do you minimize the time spent and maximize the information retrieved? How can you be sure that you recorded the URLs [Internet addresses] correctly? How can you speed up the process? The answer to all of the above questions is to make and use a log.

A log is an incredibly handy tool and quite easy to set up. Open a page in your favorite word processing program or notepad. [I recommend a recent version of Word, because you can automatically turn URLs into active links by using return/enter at the end of the address.] It is easy to toggle between windows or to size them to see more than one at a time. Experiment a bit to find a system you like.

When you find something you want to save, be it a single address or a whole page of information, you can simply copy/paste between the browser and your log. You can add your own notes and comments as you go, note questions you have, ideas you want to follow in the future, and so on. Be sure to save your log to a disk. If using school computer labs, the log has an additional advantage for bookmarks. Since bookmarks are regularly removed from lab computers, the log allows you to carry your bookmarks to any machine you want. [Note: Zip drives are becoming the standard. Some machines have 100 MB drives and others have 250 MB drives. Both types will read/write on 100 MB, so that is the best size of zip disk to get.]

The log can be advantageous for completing assignments. Besides editing them for your own use and making them functional accessories to surfing, you can use them to store material for answering homework questions and for projects. It is easy to copy/paste onto another page and then do a little editing.

A word about printing: If using on-campus computers in computer labs, you only need to provide your own paper for the printer in the lab, or you can e-mail stuff home to print on your own printer. If using computers in the library, you can either pay ten cents/page or you can use e-mail, which is cheaper.

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Focus of Computing Exercises:

Computing exercise 1 has two main objectives. First, it provides a basic introduction to useful sites related to virology. In addition to providing sites, there is instruction on how to go about finding sites of interest by using search engines. Developing efficient search strategies early will help in many ways throughout the semester, and beyond. I encourage everyone to extend beyond the limits of the exercise by exploring some other links given on the "Links" page.

Second, it provides an introduction to computer-based molecular modeling. Previewing the molecular model pages at the Kuby & Lodish interactive sites will give you a taste of what you can do. In the exercise, instructions are given on how to find and view molecular models of proteins. As we progress in the course, you may find it useful to look up the structure of some of the specific proteins discussed.

Computing exercise 2 introduces you to the basic core of molecular bioinformatics, which includes locating specific nucleic acid and protein sequences, searching for homologous sequences and making alignment maps, and looking for homologies among a selected group of sequences. The power of computers and quality application programs have made these tasks quite simple when compared to what could be done just a few years ago. This is an area where a "long, long time ago" and "once upon a time" means only 10-15 years. You will find keeping a log quite valuable in this exercise.

Computing exercise 3 is your chance to utilize what you have learned in the first two exercises and apply it to a topic of your interest. This is intended to be a short project using bioinformatics tools and techniques to answer a question related to virology. You need to design your project, find the data, run the analysis, and write a short report.

After all three exercises are completed, there will be a survey on this portion of the course. You will earn points for completing the survey, but the content of the survey results are anonymous. I will use the results to improve future offerings of the exercises.

Access to these exercises can be done either by using the links at the top of the page, or from the index. I recommend using the exercise on-line; that way, you only have to click on the active links. However, they are set up so that you can print them out, and manually enter the URL's. An alternate approach would be to copy the contents of the exercise into your log, then just work from one browser window and the log. This is advisable if you have limited RAM or if you have problems running multiple windows.


The Great Paper Chase

Although a separate assignment not focused on bioinformatics per se, the Paper Chase does require computer search tools and strategies. The primary search resource for this is PubMed, available through NCBI. Other literature search engines are available to you as well. Use of a log here can save time while hunting for listed citations or in making requests for copies of specific papers. You will also learn how to search for on-line journals and to directly download full-text papers off the web.

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Interactive Virology Using WebCT

On the second day of class, you will be given your ID and password. You may change your password to suit your needs. You may also select a global ID and password, if you have several WebCT accounts, which is easier than trying to remember several passwords. To do that, go to the WebCT homepage.

You will have the opportunity to exchange news and views via the course email [like a list-serve] and in discussion fora. If your study group wants on-line access, that can be arranged.

For a general guide to using WebCT, go to:

http://www.sonoma.edu/people/cochran/edu480/webct_guide.html

Check back here for updated information regarding tips, tricks, and changes specific to this course. Announcements will be made on the homepage to let you know if there is something new.

 

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 Updated 3/4/02 by thatcher@sonoma.edu